The 2012 extent has fallen to 3.41 million sq km, which is 50 per cent lower than the 1979-2000 average.
Arctic sea ice has long been regarded as a sensitive indicator of changes in the climate, NSIDC said in a statement.
Scientists who have been analysing the startling melt think it is part of a fundamental change.
"We are now in uncharted territory," said Mark Serreze, director of the National Snow and Ice Center (NSIDC) in Colorado, US.
"While we've long known that as the planet warms up, changes would be seen first and be most pronounced in the Arctic, few of us were prepared for how rapidly the changes would actually occur," said Serreze.
This year's minimum caps a summer of low ice extents in the Arctic.
On August 26, sea ice extent fell to 4.10 million sq km , breaking the previous record low set on 18 September 2007 of 4.17 million sq km.
It fell below four million sq km on September 4, another first in the 33-year satellite record.
"The strong late season decline is indicative of how thin the ice cover is," said NSIDC scientist Walt Meier.
"Ice has to be quite thin to continue melting away as the sun goes down and Fall approaches," Meier said.
Scientists say they are observing fundamental changes in sea ice cover. The Arctic used to be dominated by multiyear ice, that survived through several years.
The region is characterised by seasonal ice cover and large areas are now prone to completely melt away in summer.
The sea ice extent is defined as the total area covered by at least 15 per cent of ice, and varies from year to year because of changeable weather.
However, ice extent has shown a dramatic overall decline over the past 30 years.
NSIDC lead scientist Ted Scambos said that thinning ice, along with early loss of snow, are rapidly warming the Arctic.
"This will gradually affect climate in the areas where we live," Scambos said.
"Recent climate models suggest that ice-free conditions may happen before 2050, though the observed rate of decline remains faster than many of the models are able to capture," NSIDC scientist Julienne Stroeve said.
